Lugia vs Shadow Lugia
by shadowlugia249
Summary: Original Story! Ash Ketchum meets the hero of Pokemon XD, and with the help of a young Lugia named Silver, they must overthrow Cipher one last time. Match of the Century: Lugia vs. Shadow Lugia! Now updated.


**Lugia vs. Shadow Lugia**

_By shadowlugia249_

**Chapter 1: A Cry for Help**

What if Cipher had been allowed to continue with its Shadow Pokémon plan at the end of Pokémon XD? What if Shadow Lugia hadn't been captured? What if Shadow Lugia had had a son? What if Ash and his friends had been involved? These questions have been waiting to be answered. Keep in mind that this is completely made up on the spot. However, the battle of the century has been begging to be written.

Grand Master Greevil laughed as Shadow Lugia finished off the kid that had been bothering him from the start.

"You see? No one can defeat Shadow Lugia! Even your pathetic attempts to Snag him were fruitless!"

Michael Snagem hung his head in defeat. Why did he have to use that Master Ball earlier? He should have expected this from the start.

His Pokémon had all been defeated while trying to Snag Project XD001. To make matters worse, he had run out of Ultra Balls while trying to Snag the Legendary Shadow Pokémon. It had been nearly impossible to keep Shadow Lugia in the ball for more than two knocks.

Now, it was his fault that Cipher would be free to resume its Shadow Pokémon plan. He would never forgive himself for this.

"XD001!" shouted Greevil to the purple-skinned Pokémon. "Finish him off! Shadow End!!!"

Michael could only watch as his best-laid plans were ended in a blast of shadowy light.

Deep beneath the oceans of Hoenn, a lone Pokémon swam through the underwater current that snaked its way throughout the planet. It was a long ways from its home in the Orange Islands in Johto, but the Pokémon was searching for something that it desperately needed.

It was a young Lugia searching for its long-lost parent. It had gone out on a flight over the remote region of Orre and had not returned in years. The young Lugia, named "Silver", had suspected that its father had been captured or had been unable to return after all this time.

The last thing that Silver remembered his father saying before his mind was obstructed by a shadowy aura was, _Seek the Chosen One and find Orre. Hurry, there is not much time left for me!_

This message had nearly torn Silver's heart in two when he had heard it. His father was in great danger but he had been too young to do anything about it. Now, five years later, Silver was fulfilling his father's wishes and was seeking out his father's Chosen One in the distant area of Hoenn.

From listening to the voices of the planet like his father had taught him, Silver was able to determine that the Chosen One was in the vicinity of Mossdeep City. This worked to his advantage because this limited how much time Silver would spend out of the water, thereby reducing his chances of getting caught. Silver swam on, hoping that the Chosen One would be able to help him find out what had happened to his father.

**Chapter 2: Meeting the Chosen One**

Meanwhile, Pokémon Trainer Ash Ketchum, brother and sister Trainers May and Max, Pokémon Breeder Brock and the tiny electric Pokémon Pikachu were visiting Mossdeep City's famous Space Center as a part of Ash's quest to acquire all eight of Hoenn's Gym Leader Badges. Ash and May were observing a case full of metallic meteorites that had been recovered from the moon almost 40 years ago. Max, on the other hand, had his hands full keeping Brock away from the hot girls roaming the museum.

"It says here that these meteorites were discovered in a crater spanning over three football fields in length," said May, reading off the card on the display.

"Wow…" said Ash, thinking about how long that was. "That's _really_ long."

"Pikachu!" piped the electric Pokémon from atop Ash's cap.

May's stomach started to rumble. She laughed nervously and said, "I wonder if this place has a concession stand or something. I'm starving!"

Ash also was in need of food. "I guess we can take a short break. Where's Max and Brock?"

The persons in question were engaged in an ear version of Tug-o-war. Brock had tried to woo a pretty girl with orange hair. Max had thwarted his plans by seizing Brock's ear as he leapt at her.

"Ahh! Not the ear!" whined Brock as Max pulled him away. "I wanted to save her a seat at a table."

"The only thing _she_ needs saving is herself from you," said Max, releasing Brock once they were far enough away from the woman.

"What's wrong, Pikachu?" asked Ash while they ate at the small diner in the museum. "You haven't touched your food."

Pikachu was looking out a window at the seaside with apprehension. He seemed to be waiting for something.

"I'm sure he's just not hungry," May suggested, taking a drink of her soda.

"I dunno about that." Ash seemed uncertain. "Pikachu's been acting really weird lately. The last time he acted this strange was when I had to save the world from destruction in the Orange Islands." He returned his attention to his cheeseburger, still keeping an eye on his Pokémon. They had just finished their meal when Pikachu's ears perked up.

"Pika-pi!" The yellow Pokémon darted out of the building with the others following behind him.

"Hey, Pikachu! Wait up!" Ash ran down the hill, tripped and tumbled to the edge of the coast.

"Ash!" called May, trying to keep from falling down like he had. "Are you okay?"

"I'm fine!" Ash got gingerly to his feet and looked around for Pikachu.

The Pokémon was running down the beach and disappeared around a corner in the cliff side.

"Pikachu!" Ash ran down the beach with May, Max and Brock far behind him. "Get back here!"

Ash found Pikachu in a small cave on the far end of Mossdeep city overlooking the ocean. He had had to climb a bit, but he soon reached the cave where a surprise awaited him.

"Lugia?!"

It was… yet it _wasn't_ Lugia as Ash remembered him. He still had the same silver-white skin, navy-blue eye masks, tail spikes and ten back plates. He still looked like a great bird of destiny with his large, broad flipper-like wings with its finger-like "feathers" on the end. Ash still recognized the digitigrade, three-toed feet and his kind, navy-blue eyes. But something told Ash that this was _not_ the same Lugia that he had met in the Orange Islands all those years ago.

His reason? _This_ Lugia was not as large as the one he had met before and its psychic voice only confirmed his suspicions.

_Hello, Ash; the Chosen One._

Lugia had had a firm yet calm psychic voice. This one had a more free-spirited voice not unlike that of a teenager. Ash could only think of one word.

"Silver?"

Ash had met Silver after the whole ordeal in the Orange Islands. He had been named that by a young kid that had found Silver separated from his parent, Lugia. While Ash was there, Team Rocket had captured Silver but was thwarted by Ash, Brock, Misty and a Dragon-type Trainer named Lance.

Silver had been too young to speak mentally back then; this kind of surprised Ash when he spoke to him, even calling him, "The Chosen One."

"What are you doing here in Hoenn?"

Silver snorted. _A decent greeting like, "Hi, Silver! It's nice to see you!" would have sufficed. Sometimes I wonder how you humans get along with lines like, "What are you doing here?"._

"Sorry," Ash said slightly embarrassed. "I just wasn't expecting to see you here. That's all."

Silver smiled and spread his wings elegantly despite the small cave. _That's okay. No harm, no foul._

Just then, May, Max and Brock climbed up to the cave. They were all surprised to see Silver.

"Lugia?!" they all said at once.

_Not quite. Ash, I don't think I've ever met your friends. Why don't you introduce me?_

"Ash, you _know_ this Lugia?" said Max, still surprised.

Ash didn't want to sound rude in front of the son of the Beast of the Sea, so he formally introduced them all.

"May, Max, Brock… this is Silver. He is actually Lugia's _son_." He turned to Silver. "Silver, these are my friends May, Max and Brock."

Silver bowed his head and held his wings up gracefully. _It's nice to meet you, friends of the Chosen One._ He paused and eyed the three of them for a moment. _Where is the red-haired one that you call "Misty"?_

Ash explained about when Misty left the team some time ago.

_I see. She was quite a decent Water Pokémon Trainer._

"Ash," said May after a while. "Will you please tell us what's going on?!"

Ash wanted to know the very same thing. "Yeah, what _is_ going on, Silver? Why are you all the way over here in Hoenn?"

Silver's mood suddenly became grave.

_My father was abducted somewhere in the Orange Islands over three years ago. He contacted me and told me to find "The Chosen One" and take him to a place called "Orre" where I lost contact with him._

All four of them and Pikachu were speechless. Kidnapping a Lugia was no easy task. Whoever did it must have had a _lot_ of time, patience, power and resources to pull that stunt off.

"Who would do such a thing?" said Brock in disbelief.

_They call themselves "Cipher",_ said Silver, a hint of venom in his voice. _They have been using technology to artificially close the hearts of Pokémon, thus producing what they call "Shadow Pokémon". The Shadow Pokémon are used as fighting machines for the Cipher, who plan to take over Orre in just a matter of months._

"That's terrible!" cried Max in outrage. "They're worse than Team Magma, Team Aqua and Team Rocket put together!"

"Yeah, whoever heard of closing Pokémon's hearts to use them as fighting machines?" May could hardly take it in either.

"Silver," asked Ash. "How do you know all this?"

"Pika-pi!" cried Pikachu in annoyance. "Pika-Pikachu Pika. Pika-Pika-Pikachu Pika!"

_Now, now Pikachu,_ said Silver, looking in the direction of the Pokémon. _I do not know everything about Cipher, but my father told me as much as he could before I lost contact with him._

"What _do_ you know, Silver?" said Ash, picking up Pikachu and letting him climb onto his shoulder. "What can we do to help?"

Silver locked eyes with Ash. The human could see the determination radiating from those narrow, blue pupils.

_I have a hunch that my father is somewhere in Orre; I can sense that he has not left the region yet. As for what you can do—I need you to travel with me to Orre and help me find out what happened to him. I will also need the help of you and your friends' Pokémon. The Shadow Pokémon that Cipher is producing are very powerful and it will take every one of you working together to defeat them._

Silver suddenly broke off and looked off to one side. He seemed to be contemplating something.

_What if he's…? No… It can't be true… He would never allow it. He'd rather die than…_

"Silver?" May walked up to Silver and put her hand on his back. "Are you okay?"

He looked at her with sadness in his eyes. _You don't think my father…?_ He didn't finish the sentence.

Ash misinterpreted what he was thinking about and spoke to him. "I'm sure Lugia would be proud of you for taking a stand against Cipher to try to save him."

This cheered Silver up slightly despite that his thoughts being on something else.

_Thank you, Ash. I appreciate your courage._ He then hopped down from the small ledge that he was on and looked at the others in turn. _May, Max, Brock, Pikachu… We must depart. I can carry two of you on my back. I'm afraid that the rest of you will have to follow me from the sea._

After some brief discussion, the four of them agreed that Ash and May would ride Silver to Orre while Max and Brock borrowed Ash's Lapras and followed from the sea.

_It's a long ways to Gateon Port in Orre,_ said Silver from the edge of Mossdeep City. They wanted to leave inconspicuously without letting anyone know that Silver had dropped by. _If I travel at your speed, it will take most of the night to reach the seaside port._

"I've never camped out at night while in the air before," said May, uncertainly. "Can you stay in the air that long?"

Silver chuckled. _You insult me, May. We Lugia could fly around the world twice without a rest if we wanted to._

May looked embarrassed. "Oops, sorry!"

_It's okay. You didn't know._

And with that behind them, Silver unfurled his back plates and spread his wings.

_You'll enjoy flying with me. Ash has done it before with my father, correct, Ash?_

Ash chuckled nervously and said, "Yeah, I guess."

The two of them laughed as Silver took to the air. They were about to journey to a region scarcely visited by outsiders. Brock and Max followed below on Lapras.

Their journey had begun!

**Chapter 3: The Dream**

Michael Snagem was reliving a nightmare. He had failed to stop Cipher and Shadow Lugia from rising to power with their Shadow Pokémon plan. His dreams were filled with a shadowy aura. It was as if he, himself was becoming a Shadow Pokémon.

And then a light parted the violet aura and Michael found himself looking at Project XD001 in a bright, sunny day. But it wasn't the Shadow Lugia that he remembered fighting. Its purple skin was now a silver-white hue and its eye mask was slightly shorter and was navy blue – the same color as his back plates, tail spikes and similarly-colored to his sky-blue belly. This XD001 no longer had the burning, soulless eyes; it had kind, navy-blue irises that warmed his heart to look at.

The creature of his dreams also had two Pokémon Trainers – a boy and a girl on its back along with a Pikachu that was strangely perched on the boy's shoulder instead of being in a Poké Ball. Below them was a Lapras that was ferrying two more Trainers – a brown-skinned man and a young boy with glasses across the ocean.

The silver-white Lugia spoke to Michael through his dreams. _Michael Snagem… We are coming to help Orre. Meet us at Gateon Port in two hours._

Michael tried to respond but his dream cut out and he found his consciousness gripping at him.

"Plus! Plusle! Plus-Plusle!"

"Minun! Min-Min! Minun!"

Michael's sister Jovi's Plusle and Minun were hopping on his bed trying to wake him up. Michael sat up and cleared his head. What a strange dream! He had never believed much in prophesied dreams before, but something told him that he needed to heed _this_ one.

"Yay! Yaaaay!!!" Plusle and Minun cheered when they saw that Michael was awake and scurried off to tell the others.

Michael Snagem got out of bed and winced. His right arm was in a sling. Thankfully, his left arm, which sported his famous Snag Machine, was uninjured. That was a good thing; he couldn't Snag any Shadow Pokémon without it.

Come to think of it, Except for Grand Master Greevil's Pokémon, Shadow Lugia and Wanderer Miror B.'s Dragonite, Michael had Snagged every last Shadow Pokémon that Cipher had created. He felt a sense of accomplishment for having shut down Cipher's Key Lair and stopping the Shadow Pokémon output.

Then he thought about his dream. He had failed to get a chance to Purify Greevil's Shadow Lugia, but he was sure that the creature in his dreams was a Lugia that had escaped Cipher's clutches. He had read about Lugia being intelligent enough to communicate telepathically with humans. The problem was that wild Lugia resided halfway across the world in the region called "Johto". He had never understood how Cipher had captured it and kept it secret while transferring it all the way to Orre. Michael figured that it must have been a different Lugia that had contacted him.

"Michael! You're awake!"

Michael's sister, Jovi and his mother, Lily came bursting into his room followed by Professor Krane and Plusle and Minun.

"Jovi has been so worried about you! Jovi thought you'd _never_ wake up!"

"How long have I been out?" asked Michael, favoring his right arm.

"About two days," said Professor Krane. "You really took a beating from Cipher."

"Two days?!" Michael couldn't believe it. "What's Cipher been doing since then?"

"Believe it or not, Cipher hasn't been heard of since we found you."

"Huh." Michael didn't believe that, but something told him that he was gravely mistaken.

About an hour later, Michael had left Pokémon HQ and was motoring over to Gateon Port on his Hover Scooter. He had told Professor Krane and Lily about his dream and had gotten their feedback on it.

"I've read about Legendary Pokémon communicating to humans through telepathy in books, but I never knew it was true."

"Are you sure it was a Lugia?" Lily had asked interestedly. "And are you sure there were people with it?"

Michael had nodded. "I'm sure of it. That dream was the clearest one that I had ever had."

Professor Krane had seemed interested in meeting a Pokémon and travelers from a different region.

"Why don't you bring them by here and we can discuss what we're going to do about Cipher?"

Michael figured that the visitors knew something about Cipher. He didn't know how, but he was sure that they were coming to help them out.

Now he was motoring across the grassy prairie towards the seaside town. He had a hunch that this dream had more credit than he was giving it. He would just have to see if dreams really _did_ come true.

**Chapter 4: Snagem Meets Ketchum**

Silver flew well into the night. Ash, May and Pikachu had fallen asleep on his back. Luckily, his body heat kept them warm enough that they didn't freeze to death. Down below, he had blown a small, blue fire on the back of Lapras' back that kept Max and Brock warm but didn't burn or harm any of them.

Silver kept flying with the confidence that his father was still alive and waiting for him somewhere in Orre. His powers of foresight enabled him to see that a young Pokémon Trainer named Michael Snagem would help him find his father. In order to recruit Snagem, Silver had sent out a message to him through his subconscious to let him know that they were coming. He had Michael meet them in Gateon Port. As the sun began to creep over the horizon, Silver could make out the edge of the region of Orre. He traveled along the coast of Orre with Lapras following beneath him until he reached the hill out looking Gateon Port.

_Ash, May, Pikachu… We are here._

Ash and May yawned and stretched as they woke up.

"Ahh… We're here already?" yawned May, climbing down from Silver's back. "That was quick."

"I didn't notice," said Ash, sliding down as well.

"Hey, Ash! We made it!" Brock came running up from the dock followed by Max.

Ash ran down to meet them and recalled Lapras to his Poké Ball. He turned around and…

Silver was gone! In his place was… a boy?! Ash had never seen him before. He was roughly about his age and wore an orange-and-brown shirt with dark-brown pants. He also wore running shoes colored brown and orange with a green tongue on each one. Ash also noticed that he wore fingerless gloves like he did, but his were orange instead of black and had a green stripe around the cuffs.

The adolescent had a brave face with navy-blue eyes similar to Silver's. Other than that, the only thing that suggested that this was not a real human was the fact that he had a head full of untidy… _silver_ hair? Around his head was a green headband with a white Poké Ball symbol on the front of it.

"Hello, Ash." The boy spoke in a vocal voice similar to Silver's psychic one. "Do you like it?"

"Silver…?"

"The one and only."

Ash noticed that May had hearts in her eyes. He walked up and waved a hand in front of her face. She soon snapped out of it.

"If I didn't know better, May, I'd say that you _like_ my human form." Silver smiled and chuckled.

"If you _were_ a real human, I would!" May sounded slightly disappointed.

"My sister has a _crush_!" sang Max, teasing her.

"Knock it off, Max! I do _not_!"

"Do too!"

"Do not!"

"People, please!" Silver intervened. "I don't mind at all."

He looked down the hill at the people scattered throughout Gateon Port. "I think I would draw too much attention to myself if you called me "Silver" from now on. It would be better if you called me "Sam" until we found who we were meeting."

"We're meeting someone?" asked Max confused.

"Pika Pika?" added Pikachu.

Silver looked blank. "I didn't tell you?"

Everyone shook their heads.

"Oh… Well, I contacted a young Trainer named Michael Snagem while you were asleep last night. It turns out that _he's_ the one who's been giving Cipher a difficult time with their Shadow Pokémon plan. I think that he could help us in our quest, so I contacted him last night and told him to meet us here soon." He looked a little further. "Ah, I think I see him now!" He pointed to the town entrance.

Four humans and a Pokémon looked where Silver was pointing and saw a single, red-haired human dismounting from a scooter.

"He looks cute," said May, starting down the hill. "Shall we go meet him?"

Michael dismounted from his Hover Scooter and parked it in its usual spot by the town sign. After putting it in its Anti-Theft Mode, he wandered around the town while he waited for the Lugia and its passengers to arrive.

He walked over to the Robo-Kyogre down by the dock that he had used to reach Citadark Island and sat down on the dock. If he knew Lugia, it would be coming from the ocean side. However, he was completely caught off guard when someone tapped him on the shoulder and said, "Michael Snagem?"

He quickly stood up and turned around. Two teenage boys, a black man, a girl, a younger boy and a Pikachu were standing on the dock next to him.

"I'm him. Who are you?"

The group introduced themselves.

"I'm Ash Ketchum. I'm a Pokémon Trainer and this is my Pokémon, Pikachu."

"Pika!" Pikachu gave Ash's trademark pose and smiled from atop Ash's cap.

"I'm May," said the girl with brown hair. "And this is my little brother, Max."

"Hiya!" The boy with glasses waved at him.

"I'm Brock," said the Black man. Michael shook his hand with his Snag Machine arm since he was left-handed. "I'm learning to be a Pokémon Breeder."

"My name is Michael Snagem," said Michael, bowing. "I'm a Pokémon Snagger."

"What's that doohickey on your arm?" asked Max, pointing to it. "It looks like a bionic arm – OUCH!"

"Be nice!" said May, stepping on Max's foot.

"Oh, this?" Michael held out his arm so that they could see his Snag Machine in full view. "This is my Snag Machine. I used it to Snag Pokémon from the Cipher Peons. I managed to capture every one…" He suddenly seemed grave. "Except one."

"Father…" The silver-haired boy spoke for the first time.

"Huh? What did you say?"

The boy looked at Michael with sad, navy-blue eyes.

"I knew it from the start. Cipher has captured my father and has turned him to Shadow."

Michael's mind was reeling. Who was this kid and how did he know of his encounter with Shadow Lugia? He hadn't said anything about it and the subject hadn't even been brought up.

"How…?"

The kid regained his composure, but a sense of loss was still in his eyes. "I'm sorry. It's just that your mind has such detailed images of my father. I can't believe that after all this time, this is what has happened to him."

Pikachu perked up. "Pikachu-Pika Pi-Pikachu Pi?"

The silver-haired boy looked at the Pokémon and said, "He can be trusted, Pikachu. I have no reason to hide anything from him."

Michael was completely lost. "Will someone please tell me what's going on?!"

Some unspoken words must have been relayed between Ash and the silver-haired boy because they looked each other in the eye and Ash nodded. Ash then turned to Michael and spoke.

"Let's go somewhere more private and we can talk about this freely."

Michael nodded dumbly but followed the Ash and the group to a secluded area in the hills behind Gateon Port.

"You have _got_ to be joking me!" Michael was not taking in a word of what Ash and the silver-haired boy were saying.

Ash, Pikachu, Michael, and the silver-haired boy were in a hidden area in the hills of Gateon Port. May, Max and Brock had gone to the Krabby Club to get something to eat.

What Ash and the boy had told him completely went against all the laws of the world that Michael had ever known: the silver-haired boy was _actually_ a teenage Lugia named Silver that had taken the form of a human.

"What kind of nut do you think I am?"

Ash and "Silver" looked at each other again.

"It seems that our friend here requires more than just our word," said "Silver".

"I guess so," shrugged Ash.

More silent words passed between them and Ash nodded and backed up to give Michael and "Silver" plenty of room.

"What the…?"

Silver turned to face Michael and suddenly started glowing a bright white. His entire frame became solid white light. The light reshaped itself to become something… _much_ bigger. Michael backed up, tripped over his own foot and fell flat on his rump. The white light soon resembled a smaller, but _very_ familiar figure. Soon, the light became solid again and Michael found himself looking up into the face of a 14-foot-long…

"Lugia?"

It was the exact same Lugia as the one that had visited his dreams the night before. It looked similar to the Shadow Lugia that he had failed to Snag but slightly smaller and colored to match the Lugia in his dream.

But that was the least of his concerns. He had just watched a human morph into a Pokémon – a clearly impossible feat.

The Lugia smiled at Michael, who was still on the ground and looking scared.

_Don't look so frightened, Michael,_ said the Lugia, using its mind to speak and not its mouth. _I'm sure I gave you plenty of forewarning before I arrived._

Michael didn't know what to say. A Pokémon had never spoken to him using clear English before, much less address him formally using his name.

He flinched as the Lugia extended its large, flipper-like wing "palm" up to help him to his feet.

_It's okay; I know you've had some bad experiences with Lugia before. I can assure you that I will not harm you. Need some help?_

Michael blinked but took its wing and hoisted himself up. Lugia felt much different than he thought they did since he had never really touched one before. Instead of the expected cold, scaly skin, Lugia felt like warm, taut, rubbery flesh. It felt just like, if not smoother than a Seel's body.

_That's better. See? We're not as bad as you think, are we?_

"No… I guess not."

Ash walked up to Michael and talked to him. "We've got a lot to talk about, friend."

**Chapter 5: Making the Plan**

Some time later, Michael knew everything about why Silver, Ash and the others had traveled to Orre. They had come to save Silver's father, but Michael put a dent in their plans by explaining that the Lugia in Cipher's possession was supposedly "unpurifiable" and therefore unable to Snag.

However, Silver saw a hole in Michael's story, and being psychic, revealed what he was hiding.

_You never said anything about having already used up your Master Ball before fighting Greevil._

Michael had tripped over his own words. "You won't say anything to anyone at Pokémon HQ, will you? I was supposed to use that Master Ball on Shadow Lugia but I must have pulled out the wrong Ball when I was Snagging a Shadow Salamence."

Silver stared long and hard into Michael's eyes to detect anything else he might be hiding. Finally, he nodded and said, _I believe you. It was an unfortunate accident. Fortunately, I have a simple remedy in the event that we encounter my father again._

Silver held out his wing in front of him and his eyes glowed a bright blue. A white orb of light materialized on the tip of his wing and soon solidified into what was unmistakably a Master Ball. He then tossed it to Michael, who looked at it in disbelief.

_Don't lose this one. It's taken me a very long time to get the power to summon this very one._

"How long?" Immediately, Michael slapped a hand to his mouth. He had just asked a very rude question to a Pokémon that was second to God in power and ability.

Silver smiled nonetheless. _It's okay. You can ask me anything. It takes over six months of solid meditation to create a single Master Ball._

He suddenly looked at Ash. _You have a question, Ash?_

Ash flinched when he was confronted suddenly by Silver. "Uh… yeah, uh…"

He swallowed and finally spilled it. "Where exactly are we going to find Cipher and Shadow Lugia?"

"Citadark Island," Michael automatically answered. "We can take my Robo-Kyogre there right now."

But Silver sadly shook his head. _Cipher is there, but Greevil and Father are long gone. They are probably halfway across Orre by now._

"How do you know?"

Silver turned and locked eyes with Michael. He couldn't look away even if he tried. _I cannot pinpoint their location, but they are somewhere in the desert. Father's Shadowed mind is obstructing their location. I don't suppose you have any knowledge as to anyone who might have ties to Cipher? _At first, Michael shook his head…

But then he remembered fighting a person on multiple occasions who had obtained stray Shadow Pokémon that had fled from their original Trainers. It seemed like a long shot, but it was worth a shot.

"Wanderer Miror B.! He's not Cipher, but he knows everything about them. From what I know, he still has one of the few remaining Shadow Pokémon left in Orre."

Silver smiled. _Very impressive, Michael. You certainly keep up to date with other things besides what comes first._

Michael blushed and shrugged.

Ash then brought up a question. "What about May, Max and Brock? I can't risk getting them caught."

_I have already thought of this. I'm afraid that your friends must stay behind while we find Cipher. I cannot risk your friend's safety. I hope you understand._

Ash's mood fell slightly, but he figured that it was all for the better."

"Great… now, then… Shall we start looking for this Miror B.?"

**Chapter 6: PKMN Trainers Ash and Michael vs. Wanderer Miror B.**

Orre was so broad that Silver was able to fly May, Max and Brock to Pokémon HQ to wait for Ash and Michael to return. Silver relayed the message to Professor Krane through Ash's friends that they would get to meet him personally when they got back.

From there, Ash and Pikachu took Michael's Hover Scooter to Pyrite Town to begin their search for the elusive Miror B. Michael had obtained a device during his first encounter with the Trainer called the "Miror Radar". Something on Miror B.'s person sent out a signal that triggered the Radar.

Silver had managed to create an identical Miror Radar to aid in their search from the air. Meanwhile, Ash and Michael would be moving from location to location on Michael's Hover Scooter. The harsh weather would make it very difficult for Ash to use his Pokémon to search from the air. Silver was the only one who could handle it because he could shield himself against the elements with his Barrier.

Some time later, Silver contacted Ash and Michael.

_My Miror Radar is going off. He's in a location called the "Rock Poké Spot"._

"I know where that is!" said Michael. He and Ash were in the area of Pyrite Town. "I caught a rare Trapinch there not too long ago. We'll be there in 15 minutes."

"Uh…" Ash wasn't so sure. "Are you sure this thing can handle the sand?"

"Handle the sand? Ash, this thing literally _surfs_ the sand! I haven't gotten stuck on this thing yet."

"Okay… Whatever you say."

Michael did a U-turn and headed in the direction of the Rock Poké Spot.

They arrived about 15 minutes later. Two young Chasers with radical-looking hair were talking to a third man. Fortunately, they hadn't noticed Ash or Michael yet.

Ash stared at the third man. He had never seen such a bizarre person before! The man was incredibly thin and about six feet tall. He was clad in a purple dancer's outfit, but that's not what startled Ash.

On top of the man's head was the biggest and most bizarre afro Ash had ever seen! It was at least two to three feet in diameter and colored red on one side and white on the other. The colors met in a zigzag down the middle of the hairpiece. Ash guessed it was fake, but he had his doubts.

"Hello, Miror," said Michael, dismounting from his scooter and casually walking up to the trio.

Suddenly, Miror B.'s cohorts noticed the pair and panicked.

"Boss!" said one of them with dyed yellow-and-orange hair. "He's back!"

"And he's brought a friend!" said the other one with black hair.

Miror B. was always moving in a groove-like dance, and he was still doing it when he turned around.

"You?!" He had a smooth, bland voice. "How do you always find us?"

"I have my ways." It was obvious that Michael had never revealed that he contained a Miror Radar. "I came here for some information."

But Miror B. didn't buy it. "Lie! You came for my Pokémon, didn't you?! Well, you've underestimated my team this time. Now, I'm going to lay the smackdown with my elegant dance steps!"

Michael sighed and pulled out one of his Poké Balls. "We always gotta do this the hard way, don't we? Tell you what: if I beat you, you tell me what I need to know, all right?"

The kid with yellow-and-orange hair snapped at Michael. "We don't take orders from you, kid!"

But Miror B. held a hand up to silence him. "Pipe down, Trudy. I've never lost a bet yet. I'm game for the little twerp's challenge." He then turned to Ash and Michael. "Deal. If I lose, I'll tell you what you want to know. Let the music play!"

From out of nowhere, dance-like techno music began to play. Miror B. did a wide backflip, landed on his hands, kept going and landed on his feet again. He then did a little dance move and let out a small firecracker at the same time that the music hit a certain beat.

"How does he do that?" asked Ash, watching the bizarre man's moves.

"You know, I never asked."

"Quit stallin', chump!" said Miror B., throwing two Poké Balls and releasing a plant-like Pokémon with a lily pad atop its head called a Ludicolo and a large, tan dragon called a Dragonite into the battle.

Before Ash could ask, Michael said, "All Trainer battles in Orre are two-on-two battles. You've done this before, right?"

Ash nodded. "A few times."

"Good. Let's get this show on the road." He selected a Poké Ball and threw it into the battle. "Go! Mightyena!"

A large, menacing black dog Pokémon burst from the Poké Ball.

Ash chose a Poké Ball and threw it into the fray. "Bayleef, I choose you!"

A pale-green Pokémon with a partially-eaten leaf atop its head and leafy buds around its neck popped out of Ash's Poké Ball.

"Baaaay!" it called out to its competition.

Ash was about to start the battle when Michael held a hand in front of him.

"Just a minute, Ash. I have a hunch about that Dragonite."

The headband-like device around Michael's head that connected to his Snag Machine whirred into life. A small glass screen slid in front of his left eye and showed some statistics.

"Oh! It's a Shadow Pokémon!"

Through the screen, Michael could see a purple aura surrounding the Dragonite. However, Ash couldn't see anything.

"How can you tell?" he asked.

"My Aura Reader is going off. Listen… Do _not_ let that Dragonite faint! I want to Snag it!"

"Isn't that stealing? It already belongs to Miror B."

"Not at all. It's much better off in my possession. Attack it, but don't faint it! I must have it!"

"Are you done yammering?" griped Miror B. "Let's get this dance on the floor! Ludicolo, Rain Dance!"

The Ludicolo spun around on its feet and did an odd dance. Almost immediately, rain started to fall, quenching the bone-dry soil.

Ash and Michael were deluged but soon fought back.

"Mightyena!" called Michael. "It's Crunch time!"

Michael's Mightyena ran forward and sank its teeth into the Ludicolo with a vicious Crunch. It held it long enough for Ash to say, "Bayleef, use Vine Whip!"

"Bay Baaaay!" Two vines sprouted from the back of Bayleef's neck and snapped viciously at the immobilized Ludicolo. Miror B. was having his butt handed to him until he brought his Shadow Dragonite into play.

"Dragonite!" he shouted. "Let's show these children how to dance! Shadow Storm!"

Ash hesitated. He had never heard of a move called "Shadow Storm" before. He got a crash course when a shadowy aura that everyone could see radiated from the Dragonite and a sudden stormy whirlwind was summoned complete with lightning. The Shadow Storm split into two miniature tornadoes and slammed into Mightyena and Bayleef. The Pokémon were hit hard and were barely able to get back on their feet.

"What's wrong with them?" asked Ash, looking worried. "It didn't hit them _that_ hard."

"Shadow Moves are super-effective against Non-Shadow Pokémon," explained Michael, also looking worried. "I can't begin to count the number of my Pokémon that I have been fainted by fairly weak Shadow Moves. _That's_ why Cipher made them!

"I'm going after Dragonite to see if I can Snag it. You take care of Ludicolo."

"Right. Bayleef, Body Slam it!"

"Baaaay… Bay!!!" Bayleef ran right at Miror B.'s Ludicolo and slammed hard into it.

"Why you—!" Miror B. was in a fit. "Ludicolo, Counter it!"

Ludicolo took in energy and launched itself at Ash's Bayleef. Bayleef went flying but was able to land on its feet. It was still in the fight.

"Mightyena, use Shadow Ball on that Dragonite!"

(Author's Note: For those of you who have not played Pokémon XD: Shadow Ball and Shadow Punch are _not_ Shadow Moves; they are Ghost-type Moves usable by most Ghost-and/or-Dark-Types. Other Pokémon can use it as well.)

Mightyena opened its jaws and a purple orb materialized in front of it. Once fully charged, it flew at the Dragonite and hit it like a mini-explosion. However, it barely seemed to phase it since the Dragonite hardly flinched and stood firm."

"Dragonite!" bellowed Miror B., still managing to keep his dancing frame going. "You don't have to take that! Shadow Rush that fool!"

Once again, the Dragonite burst into a shadowy aura, but this time, it flew at Michael's Mightyena with the force of a speeding train. Mightyena took the full force of the attack and collapsed in defeat.

"Mightyena, return!" Michael fired the Poké Ball's laser to recall his Pokémon. Choosing another Ball, he threw it into the fray. "Go, Flygon!"

A large, green, dragon-like Pokémon appeared. This one had short, three-clawed arms, striped, spiked tail, diamond-shaped wings, green "antennae" and transparent red "domes" over its eyes. It looked like a cross between an insect and a dragon.

"Wow," said Ash in awe. "You've got a Flygon!"

"I raised it from a Trapinch that I found in this very Poké Spot."

"Lucky."

Ash turned his attention back to the battle. "Bayleef, finish off that Ludicolo! Use Razor Leaf!"

Multiple razor-sharp leaves flew from the buds on Bayleef's neck, and on its command, flew at the Ludicolo. It didn't do much, but it was enough to cause it to faint.

"Ludicolo, return!" Miror B. recalled his Pokémon but did not bring out another. He then barked orders at his Dragonite. "Dragonite! Hit them with another Shadow Storm!"

"Uh-oh," Ash saw that Bayleef was about to faint. "Bayleef! Protect yourself!"

Bayleef summoned a green-ish aura and the Shadow Storm dissipated before it reached it. Flygon, however, was not so lucky. The Shadow Storm slammed into it and Flygon was knocked off its feet. Thankfully, it recovered enough to launch a bluish stream of Dragonbreath at the Dragonite.

"This is it!" said Michael, looking through his Aura Reader. "It's weak enough to try to Snag it! Wish me luck, Ash."

Ash watched as Michael held out the arm that bore his Snag Machine. A white Poké Ball symbol was painted onto the palm area and a Poké Ball materialized out of thin air and was grabbed by Michael.

"Snag Ball, go!"

He threw the Poké Ball in a way that he spun around in the air after letting go of it. The Ball suddenly exploded into a net-like energy stream unlike the ones Ash was used to. The Dragonite was reduced to a stream of light and soon disappeared into the Snag Ball, which clattered to the ground.

Now it was a game of luck. The Snag Ball had to wobble three times and click before the Dragonite was fully Snagged.

It wobbled once… and held.

It wobbled twice… good, it held well.

"Come on…" Michael was on the tips of his feet as he awaited the outcome.

Three times… a charm. Now all it had to do was…

_Click_!

"YES!!! I Snagged 'em all!"

"My beautiful Pokémon!" cried Miror B. as the music ended and he fell on his back. "My steps weren't good enough."

**Chapter 7: The Cipher Snitch**

"You actually beat me in a bet," whined Miror B. after getting to his feet. The spring had gone out of his dance step. "Well done, kid. I'm impressed."

"But… boss!" complained Trudy and Folly. "What are we going to do now?"

"I don't know." Miror B. thought for a moment. "I suppose I could always go into business with my dancing."

"Hold it, Miror," said Ash, moving to prevent them from leaving. "You owe us some information about Cipher."

Miror B. seemed willing to talk; the battle had been devastating for him. "All right, what do you want to know?"

"Grand Master Greevil escaped with Shadow Lugia from Citadark Island," said Michael. "We want to know where they're going."

Miror B. looked interested. "Did they? Well, from what I know of Greevil, he's probably headed for the north-eastern section of Orre just a few clicks from their Key Lair. Apparently, there's a new hideout up there called the Cipher Tower."

"And…?"

"_And_ you'd better be able to handle extreme weather conditions because it never stops storming over there. The sandstorms there are brutal and you can't get within two miles of the Tower without getting ripped apart by the winds."

"If it's inaccessible," Ash wondered. "How do _you_ know about it?"

"Pika!" Pikachu agreed.

"I have my ways." Miror B. didn't seem too concerned about it. "The point is that you need something fast and powerful to make it through the storms surrounding Cipher Tower. Once you break through, though, it's a cakewalk."

Michael thought about this for a while. If they were going to get through the storms surrounding Cipher Tower, they were going to need the power and the Pokémon to handle the extreme elements. Something like…

Michael's eyes glittered as he reached an idea.

"Okay, Miror B. Is there anything else you want to tell us?"

"As a matter of fact, there is." Miror adjusted his afro and said, "There's a _ton_ of security at the tower. You'd better keep your voice down and your stomachs in if you don't want to set off the audio and motion detectors.

"There is some good news, though. Greevil has probably got enough security devices in that tower that he doesn't need to rely on his Peons to do his dirty work."

"_That's_ a relief!" said Ash, taking off his cap and wiping his brow. This heat was really getting to him.

"You're free to go," said Michael, moving Ash aside. "If I need more information, I'll be sure to find you."

Miror B., Trudy and Folly made to leave, but Miror. B stopped short.

"I do have one question for you, kid."

"Which is…?"

"How do you keep finding me?"

Michael shrugged but Trudy and Folly squirmed uncomfortably. Unfortunately, Miror B. saw them.

"Do _you_ know anything about this, boys?"

"Uh… no, sir." Trudy and Folly weren't very convincing.

"There's a tracking device in your hair." Everyone whipped around.

Silver, a.k.a. "Sam", had just arrived at the Rock Poké Spot and was leaning on Michael's Hover Scooter, looking smug.

"Say WHAT?!" Miror B. couldn't believe that he had been bugged this whole time. He rounded on his cohorts and gave them a royal chewing. "You've been tracking me all this time, and you didn't say anything?!" Trudy and Folly ran for it with Miror B. in hot pursuit. "Wait'll I get my hands on you! I'm gonna give you both such a pinch!"

Michael, Ash and Silver were in stitches as they saw the trio run off into the desert. After they settled down, Michael confronted Silver. "And just where have _you_ been?"

Silver shrugged and ruffled his silver hair. "I've been here, watching you. You two battle quite well as a team. I've seen very few tag-team Trainers battle as well as you do."

Ash took this as a compliment since he managed to impress a Legendary Pokémon as powerful as Silver. "Thanks!"

Michael then pressed Silver on what he had heard while he was "hiding".

"I heard every word," Silver told them. "If my hunch about Cipher is correct, then they couldn't have picked a more isolated spot to hide out."

"Yeah. We need to find some way to get through the sandstorm to reach Cipher Tower."

"I would fly you there, but the sandstorms are way too brutal for me to keep you on my back while I dodge the winds." He let out a sigh. "Other than that, there isn't a whole lot that I can do. Unless…" He seemed to have a thought. "There _is_ something I've always wanted to try…" But the idea seemed not to work because he added, "It's probably too dangerous to try on humans."

"What is it?" Michael welcomed all ideas. "Maybe we can help."

Silver reached into his bag and pulled out what looked like a pair of regular Poké Balls. However, there was a symbol shaped like a shattered star on the tops of them.

"These are experimental Poké Balls that my father was working on some time ago to help transport humans who did not have Flying or Water-type Pokémon. However, he disappeared before we could test them."

"What are they?" asked Ash, taking one of the Balls and examining it."

"They're called "Terra Balls"." Silver gave Michael the other one. "They're like Poké Balls but work in reverse. They can hold a single human each."

"What?! I don't want to be caught!" Ash didn't like the very idea of being bound to a Pokémon like _his_ Pokémon were bound to him.

"That's not a problem. The Terra Ball does not "capture" you. It's merely a transport vessel that we Lugia were working on should we ever need them. It's just that we never got the chance to actually try them out."

Ash and Michael were faced with a decision: risk going into the untested Terra Balls and go with Silver through the force of the storm or take a detour and find a safer alternate route.

**Chapter 9: Shadow Lugia Attack**

But before either of them could answer, Silver suddenly went rigid. He looked like he had seen a ghost.

"Silver?" Ash wondered. "What's wrong?"

Silver's voice sounded scared out of his mind. "He's here."

"What?!"

"Uh… Ash?" Michael looked up at the sky and so did Ash and Silver.

The sky was suddenly filled with dark, purple storm clouds. The wind picked up and was soon blowing hard.

"He's here!" said Silver again. His expression was that of pure terror. "He can't find me here! I can't be seen!"

"Quick! Get over here!" Michael grabbed Silver's arm and ran to an outcropping of rock where they could hide. "Ash, come on!"

Ash grabbed Pikachu and made for them when a loud shriek stopped him dead. From out of the clouds came the mammoth figure of Shadow Lugia. The Shadow Pokémon soared down on the Rock Poké Spot in search of something.

"Ash, move!" Michael was trying to get to Ash, but Silver seemed to be having a seizure.

"No!" Silver was holding his head as if fighting off invisible demons. "I won't serve you! You won't turn me to Shadow! I will fight you! You won't conquer me!!!"

Just then, Shadow Lugia spotted Ash. It roared and swooped down on him. Ash couldn't move. He had locked eyes with the Shadow Pokémon and stood paralyzed to the spot. Even Pikachu's Thunderbolts couldn't budge him.

Shadow Lugia landed on the ground several yards from Ash. It stared at the human with its evil red eyes. The human then did the unthinkable. He started walking toward Shadow Lugia as if in a trance. Despite Michael's shouts and Pikachu's attacks, he kept walking toward the demonic Pokémon. He then dropped to his knees and watched as Shadow Lugia lowered its head as if to take a chomp out of him.

Michael couldn't take it anymore. "Flygon! Typhlosion! Go!"

Flygon and a large bear-like Fire Pokémon burst from their Poké Balls and ran at the mammoth Lugia. Flygon took to the air and fired a stream of Flamethrowers at it. Shadow Lugia's attention towards Ash was diverted and it turned to face Michael's Flygon.

Meanwhile, Typhlosion had stepped in front of Ash like a Pokémon shield and sent a five-point Fire Blast at the Lugia. It retaliated by absorbing the impact of the attack and lashing out with its tail. Typhlosion went flying but the spiked tail just missed spearing Ash.

Michael decided to leave Silver and run to Ash's side. He struggled a little in the blowing wind but soon reached Ash.

"Come on, Ash! Snap out of it!" He saw that Ash's eyes were slightly clouded over with purple mist, but it soon disappeared as Ash finally came to.

"Wha… what happened? Where am I?" He seemed dazed and confused.

"You're in extreme danger, Ash! Come on!" Michael grabbed his arm and ran back to their hiding spot.

All of a sudden, Michael's Flygon came crashing to earth just feet from their current location after taking the full force of Shadow Lugia's Shadow Blast.

"Flygon!" He pulled out a Poké Ball and recalled it. Now it was just Typhlosion one-on-one with Shadow Lugia…

…Or was it? A ray of clear energy came out of nowhere and slammed into Shadow Lugia. Soon after that, a smaller, but more pure Lugia named Silver launched itself at its Shadow counterpart. Shadow Lugia shrieked and wrestled Silver to the ground, pinning him under a massive, violet wing. It looked like Shadow Lugia was about to capitalize, but Silver kicked his legs out from under him, leveling him. Silver then rolled out from under him and took to the sky. After recovering, Shadow Lugia followed suit.

After recalling Typhlosion, Michael and Ash watched as the two behemoths battled it out in the sky. From what they could tell, Silver was avoiding looking directly into Shadow Lugia's eyes. Nevertheless, that didn't stop him from sending powerful Aeroblasts in his direction one after another. Silver took a Shadow Blast to the chest but dodged another and rocketed after his opponent.

Shadow Lugia was getting frustrated since it had been hit by two Aeroblasts and had only hit Silver once. Eventually, it was able to branch off of the fight and head in Ash and Michael's direction. They barely saw it coming and it cost them dearly. Shadow Lugia opened its beak wide and seized Ash around the waist, bringing him into the air.

"Silver, help!!!" Ash was pinioned in-between Shadow Lugia's jaws gently enough not to hurt him but firmly enough that he couldn't move.

Silver saw that Ash was in trouble and took off after them. He couldn't attack Shadow Lugia without hurting the human, so he would have to get him to drop him at catch him as he fell. He tried to get in front of Shadow Lugia and force him to land or drop Ash, but he saw him coming and turned his head to look at him.

Instantly, Silver's wings locked up as every muscle in his body froze. What he saw in his Shadowed father's eyes was so chilling and terrible that Silver actually let out a Lugia equivalent of a scream and dropped from the air. He had failed Ash and he had failed his father as well.

**Chapter 9: Cipher's New Plan**

Grand Master Greevil paced back and forth atop his new hideout. He was awaiting the return of XD001 so that he could press ahead with his new plan. His Shadow Pokémon plan bit the dust, but his new Bio-Pokémon Plan would be ready to go once he had acquired the subject that XD001 was retrieving for him.

He had been impressed with that red-haired kid's prowess while Cipher had been in power. He, alone, had derailed everything that Greevil had thrown at him. Kidnapping Professor Krane, the Data ROMs, the Key Lair, and every last one of his Peons had fallen at the hands of this single kid. This was _exactly_ why he wanted him as the star test subject in his Bio-Pokémon plan; his power and intelligence would be key in what he had planned for him.

"Warning. Warning. Shadow Lugia approaching." Greevil's computer let him know that his loyal servant was approaching.

"Excellent," he sneered, looking out the window. "Does he have the subject?"

"Data error. The subject in Project XD001's possession is not the intended target."

"What?!" Greevil was beside himself. "How could he mess this one up?!"

"Shadow Lugia's sensors indicate that a human of greater intelligence and power was at the location."

Greevil stopped his hissy fit when he heard this. "_More_ powerful than that kid? Well… this might work to my advantage. Let him in!"

The large dome atop Cipher Tower slid open and soon Shadow Lugia flew in carrying a paralyzed Ash. It set him down at Greevil's feet and bowed its head before its master.

"Normally, I would personally berate you for bringing me the wrong person, XD001, but this works _so_ much better to my advantage. Good work." He then turned to Ash. "You aren't who I expected, but you'll do just fine."

Ash tried to speak, but every muscle in his body was frozen. Only his eyes could move and they were filled with fear and confusion. Greevil snapped his fingers and a Typhlosion and a large crocodile-like Pokémon called a Feraligatr came to his side.

"Take him to our special cell and prep him for his test. I'll be down shortly."

The Pokémon lifted Ash between them and carried him off. Greevil then turned back to Shadow Lugia. He noticed that it had a burn mark that had not yet healed.

"You were attacked? Just wait there." He snapped his fingers again and a yellow-and-black-striped Electabuzz came to his aid with an odd-looking helmet. Greevil took the helmet, put it on and waved the Electabuzz off.

"Let's just see what happened to you, shall we?"

He activated the helmet and Shadow Lugia's eyes flashed as his thoughts were activated. Greevil found himself looking through his minion's eyes. After rewinding its recent memories, he was looking through its eyes at the Rock Poké Spot.

He was swooping down the Poké Spot looking for the red-haired kid. Instead, he saw the black-haired one that he had returned to the tower. The human had been unfortunate to look directly into his eyes and soon became paralyzed. Greevil sensed that this kid's energy levels were much higher than the one he had sent Shadow Lugia to retrieve; therefore, it was him that he chose to kidnap. However, he was hindered when a Flygon and a Typhlosion attacked him. After a brief scuffle, he overcame them.

He was about to take Ash when something unexpected happened. A younger, smaller Lugia tackled him. Fortunately, he managed to get on top of it but was taken out at the knees. Furious, Greevil took to the air to battle the Lugia. He expected to win, but the Lugia was much more nimble and had the advantage of a range of Non-Shadow Moves. Having had enough, Greevil broke from the fight and snatched Ash from right in front of the red-haired kid, whom he now saw for the first time.

Unfortunately, the Lugia still had some fight in it. It tailed him in an attempt to recapture Ash. Thankfully, he took him out of the air by paralyzing it by locking eyes with it.

Greevil had seen enough. He removed the helmet and put it under his arm. Well, this _was_ unexpected. There was still a Lugia in Orre. And judging from the size of it, it must have been his Shadow Lugia's son or daughter. Normally, he would send his Peons out to capture it, but since his Shadow Pokémon factory was out of commission, he would have to let this one slide. Besides, he would soon have a second Lugia at his control in due time.

Greevil then dismissed Shadow Lugia and went to the containment area where his newest Bio-Pokémon subject was waiting.

Ash had regained control of his body while he was locked up. His cell resembled a miniature habitat complete with a small lake and a cave. He wondered why he had been locked up in such a spacious cell but soon found out why after glancing at the other cells. Each cell contained a Pokémon in an artificial habitat, but others contained something much more gruesome.

Two of the cells that Ash could see contained a person that looked partially like a Pokémon! One contained a young girl that had been partially turned into an Espeon. Her skin had patches of purple fur on it, her left arm and leg had shrunk to an Espeon-shaped paw and one of her ears had been elongated. Ash was revolted to see a long, thin tail growing from her backside that split near the end.

"What's going on here?" Ash asked the person in the cell next to him. The teenage boy was still mostly human except for his spiky yellow skull and red eyes. From what he could tell, he was turning into a Manectric.

"We're part of Cipher's Bio-Pokémon experiment." Said the boy, slightly scared. "They're injecting humans with Pokémon DNA and turning us into their mind-controlled servants."

"Why would they do such a thing?" Ash couldn't believe his ears.

"Cipher has been selecting us for our talents as Pokémon Trainers. I used to be a great Electric-Type Trainer in Johto but I was kidnapped by that purple Lugia and brought here. What are you in for?"

"I was training to be a Pokémon Master in Hoenn when I was brought here by a Lugia named Silver."

"You know a Lugia? That's _really_ rare! Although, from what Cipher has been saying, a Trainer named Michael was supposed to be in your place."

"I know a Trainer named Michael," said Ash, leaning up against the steel mesh that separated them. "I was traveling with him to help find Silver's father."

"So, Shadow Lugia has a son… A lot of good that'll do us now…" He broke off suddenly.

"Are you okay?"

"Oh no, it's happening again!"

The boy suddenly looked as if he was having a seizure. He held his head and screamed in pain. Ash watched in horror as the blue and yellow fur sprouted all over his body. He could hear bones snapping as his face bulged out to form a pointed muzzle not unlike that of a Manectric. The screams of pain that he gave off would forever haunt Ash's mind.

Fortunately, the changes didn't seem to progress any further. Ash soon found himself looking at a half-formed Manectric. The kid still seemed to have his human mind intact because he whimpered in pain and mumbled, "Oh… it hurts so much."

Ash managed to stick his arm through the steel mesh and hold the boy's hand to comfort him.

"I'm here, kid. Don't worry."

The boy looked at Ash with red Manectric eyes. "It'll be over soon. I'm sure life as a Pokémon won't be all that bad."

**Chapter 10: Cipher Tower**

"Silver? Are you okay?"

Michael had found Silver in the middle of the Orre Desert. The Lugia had taken quite a lot of damage after his battle with Shadow Lugia. He felt a sense of regret that he had been unable to stop Ash from getting kidnapped. Nevertheless, he was more determined than ever to help overthrow Cipher.

First of all, he had to get Silver to wake up. The Lugia didn't have his shield up and his albino skin was highly susceptible to the scorching Orre sun.

"Come on, Silver. You need to wake up."

But Silver was still out cold. On a hunch, Michael opened up his bag and fished around for something. He finally pulled out a pointed yellow crystal called a "Revive". He didn't have any Max Revives so Silver would not be at full health when he used it. Regardless, it was his only chance to revive him.

Michael forced Silver's mouth open and inserted the Revive into it. The crystal shattered into pieces under Silver's bite pressure and the fragments dissolved on his tongue. Silver moaned and slowly opened his eyes.

"Silver! You're all right!" Michael was relieved to see him awake.

_I… I guess so. Thank you._

"Come on. We need to get you out of this sun. Can you turn into your human form?"

_I can try._

Silver closed his eyes and slowly morphed into his human form. Now the sunlight wouldn't affect him as much. He got to his feet and held his head.

"Wow. That fight took a lot more out of me than I thought."

"I'm just glad you're all right," Michael said, putting his Snag Machine hand on his shoulder. "We need to start looking for Ash."

"Ash…" Silver sounded disappointed. "I was _this_ close to getting him back." He held up his index finger and thumb to show what he meant. "I couldn't save him."

"There's still some hope, though. We need to get to Cipher Tower."

"Cipher Tower… right. Are you going to use the Terra Ball now?"

Michael nodded. "I'm ready for it." He then questioned Silver's state of mind. "Are you sure you're okay?"

Silver shook his head. "No, I'm not. The things I saw in my father's eyes will haunt me until he can be Purified. Ash was lucky; no regular mortal would still be sane after what I saw. I can't tell you, either," he added before Michael could ask. "There are no words in the tongues of humans or Pokémon to describe it."

"I'll… let it be then."

Silver took out one of the Terra Balls that he had previously shown Michael and Ash and pointed it at Michael, who stood firm. He fired a red laser at him and Michael disappeared into the ball in a flash of red light.

"This isn't so bad," said Michael to himself.

The Terra Ball had a rather cozy interior not unlike that of a well-furnished living-room. He had heard that the inside of Poké Balls adjusted themselves to fit the natural habitat of the Pokémon inside it. He never thought that _he'd_ be the one inside one before.

"Comfy?" Michael heard Silver's voice from outside the Terra Ball.

"Quite. Pokémon have quite the spoils in here."

"Good. I'll let you out when we reach Cipher Tower."

"Fine with me."

Michael went over to a comfortable armchair and picked up a book titled "An Advanced Guide to Mt. Battle". He had personally challenged the 100-Trainer gauntlet of Mt. Battle but had crashed and burned in the 75th zone after a well-aimed Ice Beam had hit his Flygon. It wasn't a bad read. It certainly gave suggestions on how to deal with Ice-type Moves.

Meanwhile, Silver had pocketed the Terra Ball and sighed. "At least it works," he said to himself. He then pocketed it and morphed into his Lugia form. It was going to be a rough ride heading through the sandstorms surrounding Cipher Tower, but he had to try. The fate of his father and of the Chosen One rested on his shoulders.

Silver took to the air. Up in the air, it was slightly cooler and he was able to avoid baking in the sands of the Orre Desert. He could spot the swirling sandstorms in the distance and began mentally preparing himself for the onslaught.

A few minutes later, he reached the first wave of storms. Even with his Barrier up, the winds were pounding against him like rocks caught in a tornado. Silver kept his eyes shut to keep the sand out of them and relied on the life-force of the Chosen One to guide him. He dipped low to avoid a strong wave of turbulence and soon broke through into the second wave.

Now the winds were showing no mercy. They pounded on his Barrier, whittling his Hit Points down bit by bit. Every so often, Silver had to stop and Recover himself in order to keep going. Flying debris such as small rocks and plants also hindered him in his quest. It was harder, but he finally broke through the second wave of storms.

_Now_ it was mass chaos with winds reaching up to 150 miles per hour. What's more, much larger debris was flying in Silver's direction. He just barely dodged a boulder the size of Michael's scooter that almost knocked him out of the sky. He was using his Barrier and Recover Moves more often now and it was barely keeping him going.

The sheer determination in Silver's heart to save his father and Ash was the only thing that kept him going. He kept going until his heart was about to burst from exhaustion. He was about to faint when he finally broke through the storm…

…into a calm, sunny area without so much as a breeze.

_Yes…!_

Silver gasped and collapsed to the sandy ground, completely winded. He felt a sense of accomplishment. No human or Pokémon alive except for his father could have endured that much weather torture. He had sand embedded in his smooth skin, making it coarse. His throat was bone-dry from thirst and he could barely open his eyes.

With his remaining strength, Silver produced the Terra Ball with Michael in it and released him from it in a burst of red light. At first, he was disappointed to be released, but then he saw the sorry state that Silver was in.

"Silver, what happened?!"

_I… held… my end… of the bargain. We're here. Go… find Ash._

"No! You helped me; now it's my turn to help you!"

Michael rummaged in his backpack and looked for his water jug. He found his 1-gallon water jug (the sun really takes a toll on you in the desert) and frowned when he saw that it was only half-full. Nevertheless, regarding his own thirst, he popped the top off and walked over to Silver, who was panting heavily.

_You… would sacrifice… your _own_ water... to save me? Water… is rare… in Orre._

"I don't care! I'm not going to let a Legendary die in this desert heat when we're so close to our goal! Now, open up!"

With Michael's help, Silver was able to force his mouth open and allow him to pour the life-giving liquid down his throat. Michael had to rub Silver's throat to encourage him to swallow. It wasn't much, but it was enough to wet Silver's throat and get him back on his feet.

_Thank you… Michael. I owe my life… to you._

He stumbled a little and nearly flattened Michael in the process.

"Careful! You shouldn't rush yourself. We need to find a place where you can rest."

_Yes… I sense… water nearby. I can turn human… but it will take… a lot of energy… to do._

"You do whatever you have to so that I can carry you to it."

Silver managed to turn to his human form, but it took a lot longer than normal. As soon as he did, he collapsed again.

"Come on," said Michael. "I'll carry you to the water. Just tell me where it is. In fact…" He released his Typhlosion for a little extra muscle. "Typhlosion, take Silver to rest. I've got to go find Ash."

"Be careful… Michael."

Typhlosion carried Silver off while Michael approached the massive steel Cipher Tower. From what he could tell, the tower was at least 20 stories tall and was over 100 yards in length. He certainly had his work cut out for him.

"Well… I might as well get started."

_Michael…_ He suddenly heard Silver's voice in his head. _I will join you when I have sufficiently recovered. Good luck!_

"Thanks."

Michael took a deep breath and headed for the entrance.

**Chapter 11: Ash the Lugia**

Ash was on tight nerves as he paced back and forth in his artificial habitat. A Gloom had appeared in front of his cell some time ago and used its Sleep Powder on him. While he was out, Grand Master Greevil had had him brought up to his Pokémon Lab. What happened there would change his life forever.

Greevil watched from an observers' balcony as a Rhydon and an Electabuzz carried a sleeping Ash in and strapped him to a table. Just then, a Peon in a white lab coat came in carrying a steel case. The Peon set the case down on a table and opened it.

Inside were three syringes with a different-colored liquid inside each one. One was blue, one was red and one was completely clear. Inside the third one was a tiny, almost-invisible microchip that could fit through the needle and enter a person's bloodstream

The Peon took the red syringe first and took it over to Ash. While he slept on, the Peon injected the red liquid into Ash's left leg. The liquid burned as it entered Ash's system, but he was unaware of it happening. The blue syringe was injected into Ash's right arm. Unlike the red one, the blue liquid was like ice as it flowed into Ash's blood. Still, he slept on.

The clear injector with the tiny microchip floating in it was next. This one was injected into the side of Ash's neck. The feeling on this one was neutral but it was still unnoticed by Ash.

Greevil smiled as Ash was carried off back to his cell. Soon, he would be at his control as the pride and joy of his Bio-Pokémon Plan. The best part about this was that the Bio-Pokémon subjects would be able to pass themselves off as regular Pokémon. He snickered quietly to himself as he left the observers' balcony to go attend to other matters.

Ash had come to with a sore body. After being confused for a while, he finally realized what had happened to him. He instinctively turned to the boy that had been turning into a Manectric only to learn that his transformation was complete and could no longer speak in human words. He _did_ see that there was a hint of recognization in the Manectric's eyes. It was as if some of its thoughts were still human. The best thing that it could do to comfort Ash was hold his hand in its paw while the chemicals worked their way through Ash's system.

"What's going to happen to me?" said Ash, who was almost in tears with fear. "What Pokémon am I going to turn into?"

"Grr... Man Manectric."

Ash had acquired a way of understanding Pikachu over the many years that they had been friends, but he had never spoken with a Manectric before, so he was on his own.

After about an hour after waking up, Ash could feel the first effects of the chemicals in his system take effect. He dropped to the ground as his body was racked with pain. He screamed as he felt the bones in his right arm snap and break. His arm started to bulge out, gaining mass and poundage. His skin stretched out and became rubber-like. His skin tone on that arm turned to a kind of silver-white.

Through the pain, Ash realized that he had been injected with Lugia DNA. He was turning into the Beast of the Sea! His inflating arm soon reduced his gloves and shirt sleeve to shreds. It soon was as big as a Lugia's but not as heavy as he thought it would be. Apparently, his bones and muscles had been reformed to accompany his new form.

While his right arm was changing, a minor transformation had started on his left one. The skin on his left hand became silver-white and rubbery, but the changes didn't go any further than his wrist. Not only that, but he felt something break in his right leg. Ash's leg shortened and his foot melted into a Lugia's three-toed footpaw.

Soon, the pain subsided and the transformations halted. But now, Ash had to adjust to his mutated body until the next wave of his transformations began. He crawled over to the small lake and looked at himself. He looked like a monster and the image of himself was emotionally powerful enough for him to start crying. He couldn't help it; he was scared. He was being turned into a Lugia and soon he would be serving Cipher in its twisted plan to take over the world.

He soon cried himself to sleep. The chemicals must have already started to affect his brain because his thoughts started to trail off into a white void. Little did he know that Michael Snagem and Silver the Lugia had reached Cipher Tower and were now making their way to save him.

**Chapter 12: Infiltrating Cipher Tower**

"Pika-Pikachu!"

Michael Snagem nearly had a heart attack when he heard Ash's Pikachu's voice from across the lobby.

"Pikachu? Where did you come from?"

"Pika! Pikachu Pika-Pi! Pikachu!"

Michael couldn't make heads or tails of what it was saying, but he DID notice the Poké Ball in its mouth. Tied to it with some silver string was a note.

"What have you got there?" Michael took the Poké Ball from Pikachu and unwrapped the note. It read:

Michael,

This Poké Ball contains a Skarmory who is a very close friend of mine. I have instructed it to assist you in your infiltration of Cipher Tower. I have learned from experience that Skarmory have very reflective metal feathers. Should you need it, you can use it to deflect lasers without setting them off. Take good care of it – I know it well enough to tell if you have.

Good luck,

Silver

Michael took the Poké Ball and pocketed it – his belt was currently full with six Poké Balls in his team. He would have to send one of his Pokémon back into the PC Storage System before he could use it.

"Come on, Pikachu," he said, picking up the small, electric Pokémon. "Let's find Ash."

At the end of the lobby was a PC Station. Michael took advantage of it and deposited one of his Pokémon to make room for the Skarmory that Silver had loaned him. He then called down the elevator, and since the floor buttons only went up to 15, he pressed the number 15 button. The elevator dinged as the doors closed and headed for its destination. Michael didn't know what to expect as he rode the lift to the 15th floor.

When the elevator reached its destination and it opened its doors, Michael saw that the floor was painted with a black-and-white checkerboard design. He stepped out of the elevator and onto a black panel. Just then, a klaxon alarm went off and a voice blared out.

"WARNING! WARNING! INTRUDER ALERT! INTRUDER ALERT!"

Before the elevator door could close and lock, Michael backed up into it and caught his breath. That was close. He hadn't expected an alarm. But then he remembered Miror B.'s warning about the tower being riddled with security.

_You should have seen that coming._

Michael was suddenly aware of a second presence in his mind. He shook his head as if to clear it, but it spoke again as he did it.

_Don't do that; you'll hurt yourself._

He suddenly realized who it was.

"Silver?"

_The very one. I noticed that you managed to trip an alarm on your first step._

"I wasn't really expecting that, though."

_I don't blame you. You weren't on your toes._

"I… uh… really didn't study how to defeat the security system."

_Don't worry about it. Greevil is very lax when it comes to security, so he only installed it on this floor. I managed to tap into Cipher's security system and I should be able to guide you through this floor._

"Thanks."

"Pika Pika?" Pikachu was confused to see Michael talking to himself.

_I am with him, young one,_ said Silver, branching his connection to him. _Now, listen to me, Michael…_

_Greevil has riddled the entire floor with motion sensors. I can tell that you saw the checkerboard-like layout, correct?_

"Yeah."

_Good. Each and every black tile has a motion sensor installed on it. To reach the other end of the floor, only step on the white tiles._

_Now try it again. I am watching you and will contact you when you reach the other side._

Silver left Michael's mind, but he could still tell that the Legendary was watching him. Picking Pikachu up and setting him on his shoulders, Michael opened the elevator door again and stepped out onto the floor.

In tune with Silver's words, he only stepped on the white panels so he wouldn't set off Greevil's alarm. He had to stay on his tiptoes because the panels were small enough to not be able to fit his whole foot on them. Soon, he reached a fork and Silver contacted him again.

_Good, you're doing great._

"What's next?"

_The fork in the hallway before you ends up at the same place. There are two different paths to take and each of them houses a unique challenge._

"What are they?"

_The path to the left contains a generator that sends out an electric charge through the floor panels on a timed routine._

"And the right?"

_A color-coded crane system that I'm sure you've faced before._

"I'm going to go with that one."

_Be careful. The checkerboard alarms are still in effect._

"I will."

Silver disconnected from Michael's mind and he skipped to the right path. He was standing in front of a round, red-colored gate with a crane picture on it. Where there weren't the checkerboard-like floor panels was a layout of glowing blue panels. Michael didn't have to be psychic or an expert on booby traps to tell that those panels were electrified!

He pushed the red gate open and climbed on the crane behind it. It ferried him over to another red gate and he climbed off safely on a white panel. He then hopped over to a blue gate and was ferried to it counterpart. When Michael tried to get off and on at a pair of yellow gates, he narrowly avoided stepping on a black panel. Thankfully, he was able to jump far enough to land on a white one.

When Michael reached the other side of the hallway, Silver contacted him again.

_So far, so good. You've done this before?"_

Michael shrugged. "Once or twice."

_Huh. Well, your last challenge involves the Skarmory that I sent you. There are several visible lasers in a grid before the elevator that goes to the next floor. Use Skarmory and I'll contact you once you're in the elevator._

"Will do." Michael took out the Poké Ball containing Silver's Skarmory and released it.

Skarmory were Pokémon that have feathers made out of solid steel. Many years ago, humans used to use Skarmory feathers to make fine swords; this just shows how sharp and powerful Skarmory actually are.

Michael noticed that _this_ Skarmory had much shinier feathers. They were more of a platinum color that the regular gray. He then realized something: this was a Shiny Pokémon! Shiny Pokémon were Pokémon with enhanced strength and were colored slightly different. Trainers would spend their whole lives trying to find the rare Shiny Pokémon without so much as a fleeting glimpse. Michael felt special to not only have seen one, but borrow one as well.

The Skarmory looked at Michael with a fierce red eye and opened its wings in order to show its pride. Where the feathers were supposed to be red, instead were blue. This only added to its beauty.

"Skar!!!"

Michael, in his amazement, decided to bow to such a noble Pokémon. "Well, Skarmory… are you going to help me?"

Skarmory nodded and took to the air. It flew off in the direction of the laser room with Michael jumping from panel to panel to catch up.

"Ho... ly… crud."

Michael was looking at the biggest collection of lasers he had ever seen. The lasers criss-crossed in a fancy diagonal pattern so that they rebounded off of the white tiles. The checkerboard tile alarms remained a constant theme. At the end of the hallway stood the elevator – a piece of cheese for a mouse caught in a maze.

"Pika Pikachu-Pi?" Pikachu didn't sound too confident.

"Yeah… what you said." Michael's confidence in clearing this final hurdle was ebbing.

"Skarmory!!!"

Silver's Shiny Skarmory opened its wings and walked forward… onto a black tile! Michael held his breath.

Nothing happened.

Skarmory wasn't heavy enough to trigger the alarm! Not only that, but the lasers merely bounced off of its polished feathers like flies, leaving enough room on either side of it for Michael to use the white tiles to cross the room. Now breathing a little easier, Michael took Pikachu off his shoulder and set him on the floor.

"Pikachu," he told him. "You're going to have to meet me at the elevator. I don't want to set off these lasers any more than you do." He then turned to Skarmory. "Skarmory, can you escort Pikachu to the elevator and then come back for me?"

Skarmory nodded obediently. It was certainly loyal to whoever was in charge of it.

Michael watched as Pikachu walked underneath Skarmory's wings and the lasers merely bounced off of its reflective feathers. Soon, Pikachu had reached the elevator and waited for him to meet it.

Now, it was Michael's turn. Skarmory wasn't tall enough for him to walk under it, and he still had to worry about the booby trapped floor tiles. It seemed like and impossible task.

He was contemplating on how to cross when he heard Pikachu using his Thunderbolt.

"Pika… chuuuu!!!"

"Pikachu, what…?!"

He froze and saw that the lasers were flickering and then disappeared! Pikachu had apparently overloaded a control panel on the wall that controlled the lasers.

"Pika, Pika-Pika!" It was obviously saying, "Hurry, Michael!"

Michael needed no second bidding. He quickly recalled Skarmory and made like the wind across the hallway. He no sooner reached the elevator and got it open than the lasers reactivated.

"Great idea, Pikachu!" complimented Michael, scratching the Pokémon behind the ears. "How did you know how to do that?"

""I" told him."

Michael nearly had a heart attack. That voice didn't come from his head – it came from _behind_ him!

"Silver! Don't _do_ that!"

Silver, aka "Sam" was standing in the elevator, looking nonchalant.

"I just thought I'd get your attention."

"Well, you got it. How did you get in here, anyway?"

"That's a secret that your little human mind wouldn't be able to comprehend."

"Oh… okay… fine with me."

"Would you press the number 17 button, please?"

"What am I, a bellboy?"

"No. It was just a little of your human humor."

Michael groaned and pressed the button. The elevator dinged and rose to the designated floor. When the door opened again, Michael's heart dropped.

**Chapter 13: Lugia Reunion**

Ash woke up in a great amount of pain. From what he could tell, he had undergone the second stage in his transformation into a Lugia. His neck had elongated and a pointed blue mask had formed around his eyes. His lower jaw along with a combination of his nose and upper lip fusing together now represented a Lugia beak. His teeth had fallen out except for two on his upper and lower jaws that had curved and sharpened into something resembling small fangs. From the reflection in the small lake, Ash could see that he still had all of his black hair with his eye masks and pointed skull sticking out of it.

Another transformation that had undergone was Ash's torso. It had swelled to a huge size, reducing his favorite jacket and clothes to tatters. He patted his sky-blue belly with his Lugia arm in concern.

Finally, he could see that he had grown a long, thick, flexible Lugia tail out of his backside complete with two navy-blue spikes near the tip. Ash instinctively felt his back with his still-human arm and felt only three or four fully-grown back plates. The others were either too short or hadn't grown in at all.

Ash felt more like a Lugia than before, but his human mind was still working. He wished that the transformation would finish so that his suffering would be over.

And as if he had timed it correctly, his body was racked with pain again. The final stage of his transformation had begun. Through the pain, Ash heard an elevator ding and someone come out. Somehow, he knew it wasn't Greevil. He managed to scream in his agony and let that person know where he was…

…or _persons_. Michael and Silver had reached the 17th floor where several Bio-Pokémon habitats were housed.

"Ash?! Is that you?"

"Michael…! Heeeaaaaooowwww…!!!"

Something bad was happening to him and Michael followed his screams to his habitat. Silver merely walked from cell to cell with sorrow in his heart.

"Ash, talk to me! Ash?"

Michael was looking at the Ash-Lugia creature finishing up its transformation. Ash's left arm had filled out to match his right one. His hair had disappeared and his head now resembled a full-fledged Lugia's. When the transformation was finished, Ash the Lugia looked at Michael with tears in his eyes.

_Michael…_ he said in his new psychic voice. _You made it._

"Yeah… I made it too late, it seems."

"Pika-Pi!" Pikachu had heard Ash's voice and came running. When it saw the Lugia in the cell behind the wire mesh, it was at a loss for words. "Pika-Pi?"

_Pikachu. It's me._

"This is terrible," said Silver, joining them. "Cipher has turned these pure-hearted humans into Pokémon for his army."

"Why would they do such a thing?" asked Michael.

"It's really very simple: power."

The trio looked down the hall at the person who has spoken. Grand Master Greevil was in his Hover Chair like he had been at Citadark Island when Michael had last seen him. His burning-yellow eyes made Michael flinch, but Silver looked at him with anger in his eyes.

"You," said Michael and Silver in completely different tones.

"Well, well… the boy who thwarted my plans and his Poké Pal.

Michael looked shocked that Greevil knew about Silver, but Silver, himself, was looking daggers at the small man.

"Where is my father, you scum?!"

"Temper, temper, Lugia. Your father is safely upstairs. I can fetch him if you want."

"I will do it myself. You will not interfere this time."

With a loud _crack_, Silver vanished into thin air, leaving Michael, Pikachu and Ash looking at him. Michael then addressed Greevil.

"If you think that I'm going to let you release any of these Pokémon into Orre, you're gravely mistaken. I'm going to stop you this time!"

"Oh, really?" Greevil sounded like he was feigning concern. "Why don't you as your "friend" what _he_ thinks?"

Before Michael could act, Greevil pressed a button on his chair. The microchip in Ash's body kicked in and he lost every last thought in his brain. There was only one word going through his mind now:

"Kill."

Against his will, Ash decimated the cell walls and began moving towards Michael, who had fallen on his seat and was crawling backwards.

"Ash? What are you doing?! Ash, don't do this. It's Michael – your friend, remember? Ash, snap out of it!"

But it was no use. From the look of his white, staring eyes, Ash couldn't hear him. Michael wanted to use his Pokémon, but fear was keeping him from acting. It was all over…

**Chapter 14: Legendary PKMN Silver vs. Shadow Lugia; PKMN Trainer Michael vs. Bio-PKMN Ash**

KA-BOOOOM!!!

Silver the Lugia came crashing through the side of Cipher Tower and decimated a good two or three Bio-Pokémon cells. His father, Shadow Lugia had just hit him with a very powerful Shadow Blast and sent him careening into the tower. Fortunately, it was enough to distract Ash and allow Michael to launch a counterattack.

"Typhlosion, Mightyena, go!" Silver had given Michael's Typhlosion back to him while in the elevator.

Michael's Pokémon were able to distract Ash long enough to allow Michael to tend to Silver.

"Silver, are you all right?"

_This battle is between my father and I. If I fail, you will have to Snag him. There is not much time before our battle destroys this tower and the Bio-Pokémon subjects inside. I can save them if you buy me a little time._

"I'll see what I can do."

_Good. You must distract my father and Ash until I give you the signal._

"Okay. I'll do my best."

Silver nodded and turned back into his human form. Meanwhile, Shadow Lugia had come to investigate its work. While Typhlosion and Mightyena were dealing with Ash, Michael had to send out his Flygon and Salamence to work as a tag-team to keep Shadow Lugia occupied.

All the while, Greevil was jumping up and down on his chair, screaming, "Stop them, XD002!!! Stop them!!!"

Ash, aka XD002, finally broke free from Michael's Pokémon and started towards Michael. Michael, who saw him coming, jumped on his Salamence and flew off with his Flygon through the hole in the tower, just barely missing Shadow Lugia.

Now he had _two_ demons on his tail: Shadow Lugia _and_ Ash the Lugia. He knew pretty well that he couldn't fight them head-on; he just had to stall for time until Silver had dealt with the other Bio-Pokémon.

"Flygon!" he called from atop his Salamence. He noticed that the storms around the tower had suddenly vanished. "I'll deal with Ash; you distract Shadow Lugia! Just don't fly over any towns!"

"Braaaa! Braaaa!!!" Flygon called to let him know that he understood.

The two of them split up. Michael, Salamence and Ash went west toward Mt. Battle while Flygon and Shadow Lugia flew north.

"Whoa!!!" Michael had nearly been hit by an Aeroblast fired by Ash. In an effort to slow him down, Michael reared his Salamence around and sent a Flamethrower his way.

But it was useless. Ash had absorbed the Flamethrower by using his Barrier at the right time. All Michael had done was slow himself down.

"Any time, Silver," he told himself. But Silver was apparently not done yet. Regardless, he barrel-rolled to the right and continued flying.

Just then, another Aeroblast slammed into Salamence and Michael was unseated from his Pokémon. He fell through the air towards the Orre Desert. There was no way that Salamence was going to recover and catch him in time. It was over.

_Michael!!!_

Like the voice of an angel, Silver the Lugia came rocketing towards him and snatched him out of the air by rolling on his side and tucking him under his wing.

"Silver?! You saved my life!"

_Yes, I did. A favor for a favor. But I must get you somewhere safe. Father has defeated your Flygon and is headed in your direction._

"You can't fight them both by yourself! You'll be killed!"

_I don't have to. I destroyed Cipher Tower and Ash should be regaining control of his mind soon. Now I must defeat Father and end Cipher's legacy for good._

"What happened to my Pokémon?"

_I have brought them and the Bio-Pokémon to Phenac City. They are safe now._

"But what are you going to do with me?"

_Nothing. Ash is._

"Silver, what—AHHHHHHHH!!!"

Silver had dropped him clear into the blue! Why did he do that? Michael thought that Legendary Pokémon were supposed to _prevent_ death to those that they watched over.

However, Silver's actions became clear when a similar Lugia caught him right out of the air.

"Ash?!"

_Yeah. I don't know what Silver did, but he freed me from that mind control. I can take it from here."_

"I hope you know what you're doing!"

When Ash and Michael landed in Phenac City, they watched from the below among the other spectators while the two titans battled it out from high above them.

Silver and Shadow Lugia were now engaged in a shield version of "Tug-o-War". Silver had conjured his classic clear Barrier while Shadow Lugia had created a shadowy-colored one and the two of them were slamming into each other. Every time they collided, a miniature sonic boom rang out like a thunderclap.

Hit after hit after hit echoed throughout all of Orre before both Titans realized that neither of them were going to win this way. Silver then switched to alternating between using his Aeroblast and Recover Moves. Shadow Lugia, though, took a complete offensive tactic. It either would fire off Shadow Storms at the constantly evading Silver or try to rush at him with its Shadow Blast.

Both titans were taking hits and it was quickly adding up. At this rate, they would both kill each other before the battle stopped.

Silver then remembered the Master Ball that he had given Michael. If he couldn't end this battle peacefully, he would have to make the sacrifice of his father being Snagged.

_I can't stop him!_ he called to Michael. _There's only one other way. You must Snag Father so we can end this fighting!_

"But I don't want Lugia to have to answer to a human!" said Michael from down below. "There must be another way!"

_We can possibly reverse it later; just Snag him when I come down!_

"All right!"

Silver then turned his attention back to the fight. Shadow Lugia had vanished from his line of sight! He couldn't see him anywhere!

Silver, _LOOK OUT!!!_ came Ash's voice from below.

Silver turned too late to see Shadow Lugia hit him with a particularly powerful Shadow Blast. His Hit Points went down to zero as he fell from the sky with Shadow Lugia in hot pursuit. With a tremendous _whomp_, a fresh sandy crater appeared outside Phenac city with Silver smack dab in the middle of it. Shadow Lugia landed nearby and put its clawed foot on him, letting out a screech of victory. It began to lower its head for the final kill.

"Snag Ball, GO!!!"

From out of nowhere, Michael ran to the edge of the sand crater and activated the Snag Machine on his arm. The purple Master Ball that Silver had given him flew into the crater and enveloped Shadow Lugia in its foolproof net. Three wobbles and a click later and it was all over!

Cipher was defeated, Shadow Lugia had been Snagged and the fighting was finally over. Good had won!

**Chapter 15: Purifying Shadow Lugia**

"Hey, Silver. Are you feeling all right?"

Michael sat next to the behemoth Pokémon in the Poké Center. It had been two days since Shadow Lugia had been Snagged and Michael was getting ready to head back to Pokémon HQ to begin its Purification Ceremony.

_Hi, Michael._ Silver lifted its head out of the pool that had been constructed to keep him hydrated. _Leaving already"_

"We're just waiting for you."

_Oh? Any special reason?_

"I dunno," shrugged Michael. "I just thought that you would want to be the first thing that Lugia sees once he's purified."

These words had a noticeable emotional effect on Silver. The Legendary smiled and wiped a tear from his eyes.

_You would do that for me?_

"Sure, why not? So, what do you say; are you coming?"

Silver got gingerly to his feet. _I suppose that I have sufficiently recovered enough._

"Good. Well, I'll meet you there."

Ash decided to come back to Pokémon HQ with Silver and Michael. He wondered what his friends would say when they saw a Lugia in the place of their friend and leader. He guessed that he would have to deal with it when it came.

But then he got a hint from Silver that his "condition" and all of the other Bio-Pokémon could be reversed.

_My father knows all there is to know about these cases. He's been able to repair the lives of humans _and_ Pokémon that have been transformed. We'll just have to see if he remembers how after the Purification Ceremony._

Ash's heart leapt at these words. Maybe all wasn't lost yet.

Ash and Silver arrived about 30 minutes before Michael did since he had gone back for his Hover Scooter. When they landed on the front lawn of Pokémon HQ, the people inside practically flooded out to see them.

Ash's friends couldn't believe that Ash, himself, had become a Lugia. May asked if he would take her on a moonlit flight over the Hoenn Sea. Ash had blushed at this and had "accidentally-on-purpose" knocked her over with his wing.

Professor Krane had never seen a real-live Lugia before and therefore had a lot of questions to ask Silver. Silver didn't mind; he had drawn a lot of attention to himself by showing up like this.

Eventually, Michael Snagem arrived on his Hover Scooter, looking triumphant. He was hailed as a hero for successfully Snagging Shadow Lugia and helping defeat Cipher.

"Jovi knew you could do it!" cried his little sister, giving him a back-breaking hug. "Jovi always believed that you'd come home one day!"

"Now, now, Jovi," said Lily, pulling the two apart. "Give him some room to breathe."

"Thanks, Mom," Michael said, blushing.

Professor Krane finally stepped it. "Well, Michael… Shall we get the Ceremony started?"

Michael nodded and every human piled into the building.

"What a weird machine!" said Max, looking at the massive collection of wires that all connected to the pad in the middle of the room.

"It's our state-of-the-art Purification Chamber," said Professor Krane with pride. "Normally, you can access it at any PC Station, but it's far more potent if you bring your Shadow Pokémon here.

"Speaking of which, are you ready to give it a try, Michael?"

Michael nodded and took out the Master Ball that held Shadow Lugia in it. "Let's see if this thing lives up to its name." He stepped onto the pad. "Hit me."

Professor Krane and Lily nodded and threw the controls into action. The pad glowed brightly and the lights dimmed. Soon, Michael was surrounded by holograms of Pokémon that he had already put into the Purification Chamber to get a maximum Tempo going. He took the Master Ball and opened it up so that Shadow Lugia was in the center of the circle.

He then noticed something. "Shadow Lugia is behaving rather strangely."

The Pokémon in question looked as if it was fighting off unwanted demons. Its head was moving in an odd fashion. Nevertheless, Michael signaled Professor Krane to activate the Purification process.

Suddenly, the whole room began to rumble. The power was flickering and Shadow Lugia had frozen in its place.

"A-a-are you s-sure it's supposed to do that?" stuttered May as the vibrations continued.

"I've n-n-never seen it d-do that b-b-before," Professor Krane said, trying to regain control of the machine.

"Wait, look!" Brock pointed to the hologram of Shadow Lugia.

Shadow Lugia was suddenly surrounded by a white light. It intensified and a violet aura seemed to dissolve around it. With that, Shadow Lugia became Lugia once again. His skin tone changed from purple to the classic silver-white, his eyes changed from red to navy-blue, his belly, back plates, eye masks and tail spikes all reverted to their original colors. Finally, his clawed feet were rounded toes once again.

Shadow Lugia, the Pokémon that was supposedly unpurifiable, had been Purified!

Ash and Silver waited for the aftermath of the Purification Ceremony. They had seen the lights flicker and blink as _something_ was going on in there. They didn't have to wait long before Michael and all the others came out of the building looking triumphant.

_Well?_ asked Silver. _Did it work?_

Michael smiled. "Why don't you ask your father that personally?"

He threw the Master Ball and the newly Purified Lugia appeared. The behemoth Pokémon stood over all of them and opened his eyes. The first thing that he did was look up at the cloud-free sky and smile.

_I can't remember the last time that I had seen the sky so beautiful before,_ he said, taking a deep breath.

He then noticed Silver for the first time.

_Silver? Is that you?_

_Hello, Father._

Words could not describe the connection that was felt between the father and son Pokémon. They merely embraced each other for the first time in years. The humans and Ash and Pikachu watched as a bright aura surrounded the two behemoths and then dissipated.

The two Guardians of the Sea had been reunited.

Lugia released Silver and looked at the people gathered there.

_Thank you for all you have done. Silver has indeed grown up since the last time I saw him. If there's anything that either of us can do to repay you, please don't hesitate to ask._

Ash stepped forward nervously. _Lugia, can you do something about me and the other Bio-Pokémon?_

Lugia looked at his Bio-Pokémon counterpart and smiled.

_Ahh, my Chosen One. Of course. I can help you out._

**Chapter 15: Going Back**

Lugia and Silver were able to return Ash and the other Bio-Pokémon to their original forms… but at a price. The chemicals that Cipher had injected into their bodies had been there too long. Ash and the others could return to their human forms, but they would always be able to turn back into their Pokémon forms at will.

This was more of a plus than anything else. For example, Ash could turn into a Lugia anytime he wanted in order to carry his friends and Pikachu over great distances. What's more, they could harness their forms' special abilities and Moves to use anytime they wanted.

Several days later, Ash and his friends were in Gateon Port getting ready to ride Lugia and Silver back to Hoenn and say good-bye to Michael. They had been through a lot together and it was always difficult to say good-bye to a new friend.

"I always wondered what lies beyond the sea," said Michael, looking out into the ocean. "You guys are the first people to visit from another region."

"If you ever wanted to visit Hoenn," said Brock, packing a lunch for everyone. "It's less than a day's flight to the southwest."

"Yeah," agreed May. "If you head in that direction, you'll reach Mossdeep City in no time."

"I'll keep that in mind." Michael nodded and turned back to his friends. "It's been nice battling with you, Ash Ketchum. Hopefully, you should know a little more about tag-team battles."

"Battling Miror B. taught me a lot," said Ash, his navy-blue eyes glittering. It was the only change in his appearance to show that he was part-Lugia. "I'll be unstoppable when I face Tate and Liza in Mossdeep City!"

_It's time to go, Ash and friends,_ said Lugia, checking the wind with his wings. _We need to leave now if we plan to reach Mossdeep City by dusk._

"All right." Ash turned to Michael and extended his hand. "See you later… friend?"

"Sometime… friend." Michael extended his right hand and shook Ash's.

The group climbed aboard either Lugia or Silver and waved good-bye to Michael and Orre. The Legendaries took to the air and departed from Orre. Michael watched as they disappeared into the horizon. It wasn't really good-bye; they would see each other again someday. And if they didn't, their friendship would always cover the distance between their worlds.

**END**


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